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  Eduard Ocaña-Pallarès, Tom Williams, David López-Escardó, Alicia Arroyo, Jananan Pathmanathan, et al.. Divergent genomic trajectories predate the origin of animals and fungi. Nature, 2022, 609 (7928), pp.747-753. ⟨10.1038/s41586-022-05110-4⟩. ⟨hal-03820663⟩
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  Andrew B. Watson, Romain Lannes, Jananan S Pathmanathan, Raphaël Méheust, Slim Karkar, et al.. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Evolutionary Genomics, pp.271-308, 2019, ⟨10.1007/978-1-4939-9074-0_9⟩. ⟨hal-02324786⟩
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  Raphaël Méheust, Andrew K Watson, Francois-Joseph Lapointe, R. Thane Papke, Philippe Lopez, et al.. Hundreds of novel composite genes and chimeric genes with bacterial origins contributed to haloarchaeal evolution. Genome Biology, 2018, 19, pp.75. ⟨10.1186/s13059-018-1454-9⟩. ⟨hal-01830047⟩
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  Raphaël Méheust, Debashish Bhattacharya, Jananan S Pathmanathan, James O Mcinerney, Philippe Lopez, et al.. Formation of chimeric genes with essential functions at the origin of eukaryotes. BMC Biology, 2018, 16, pp.30. ⟨10.1186/s12915-018-0500-0⟩. ⟨hal-01761411⟩
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  Eduardo Corel, Raphaël Méheust, Andrew K Watson, James O Mcinerney, Philippe Lopez, et al.. Bipartite Network Analysis of Gene Sharings in the Microbial World. Molecular Biology and Evolution, 2018, 35 (4), pp.899-913. ⟨10.1093/molbev/msy001⟩. ⟨hal-01798030⟩
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  Guillaume Bernard, Jananan S Pathmanathan, Romain Lannes, Philippe Lopez, Eric Bapteste. Microbial Dark Matter Investigations: How Microbial Studies Transform Biological Knowledge and Empirically Sketch a Logic of Scientific Discovery. Genome Biology and Evolution, 2018, 10 (3), pp.707 - 715. ⟨10.1093/gbe/evy031⟩. ⟨hal-01799304⟩
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  Johann-Mattis List, Jananan Sylvestre Pathmanathan, Nathan W. Hill, Eric Bapteste, Philippe Lopez. Vowel purity and rhyme evidence in Old Chinese reconstruction. Lingua Sinica, 2017, 3 (1), pp.5. ⟨10.1186/s40655-017-0021-8⟩. ⟨hal-01555483⟩
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  Richard G Dorrell, Gillian Gile, Giselle Mccallum, Raphaël Méheust, Eric P Bapteste, et al.. Chimeric origins of ochrophytes and haptophytes revealed through an ancient plastid proteome. eLife, 2017, 6, pp.e23717. ⟨10.7554/eLife.23717⟩. ⟨hal-01526828⟩
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  Etienne Lord, Margaux Le Cam, Éric Bapteste, Raphaël Méheust, Vladimir Makarenkov, et al.. BRIDES: A New Fast Algorithm and Software for Characterizing Evolving Similarity Networks Using Breakthroughs, Roadblocks, Impasses, Detours, Equals and Shortcuts. PLoS ONE, 2016, 11 (8), pp.e0161474. ⟨10.1371/journal.pone.0161474⟩. ⟨hal-01361753⟩
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  Eduardo Corel, Philippe Lopez, Raphaël Méheust, Eric Bapteste. Network-Thinking: Graphs to Analyze Microbial Complexity and Evolution. Trends in Microbiology, 2016, 24 (3), pp.224-237. ⟨10.1016/j.tim.2015.12.003⟩. ⟨hal-01300043⟩

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